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| Status |
Public on Jun 08, 2017 |
| Title |
S89G-AST |
| Sample type |
SRA |
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| Source name |
Astrocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Cortex
age: 10 weeks
genotype/variation: S89G-DMP1
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| Growth protocol |
Astrocytes were cultured with DMEM plus 10%FBS, and identified by GFAP immunofluorescence staining；NSC were cultured as neurospheres with DMEM/F12 plus N2 supplements, and identified by sox2/nestin immunofluorescence staining.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cultured medium was removed, cells were washed twice with PBS, and RNA was harvested using Trizol reagent. RNA library prep kit for Illumina (NEB.Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: ftp://www.icugi.org/pub/genome/cucumber/Chinese_long/v2/cucumber_ChineseLong_v2_genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jun 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bo Jing |
| E-mail(s) |
scenery126@gmail.com
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| Phone |
+8613122776193
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| Organization name |
同济大学医学院
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| Street address |
同济大学医学院713
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| City |
上海 |
| State/province |
上海 |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE99784 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes |
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| Relations |
| BioSample |
SAMN07203244 |
| SRA |
SRX2893625 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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